RaGOO-in-cwl

Wrapper tool of RaGOO by CWL and Docker

Requirements

• cwl-runner such as cwltool
• Docker
  • If you cannot use docker, this tool runs with --no-container options.
  • However, you have to install dependent tools of RaGOO, such as python3, intervaltree, numpy, and minimap2

How to use

With the CWL reference implementation (cwltool), toil-cwl-runner, or arvados-cwl-runner as your cwl-runner:

cwl-runner --outdir ${PATH_TO_OUTPUT_DIR} \
           ragoo.cwl \
           --contigs_fasta ${PATH_TO_CONTIG_FILE} \
           --reference_fasta  ${PATH_TO_REFERENCE_FILE} \

For other runners an input object is required:

inputs.yml

contigs_fasta:
  class: File
  path: path/to/file
reference_fasta:
  class: File
  path: path/to/other/file

cwl-runner --outdir ${PATH_TO_OUTPUT_DIR} \
           ragoo.cwl \
           inputs.yml

Note

As the original RaGOO implementation cannot handle with absolute file path, this tool uses modified version in the container.